High-Speed AFM Visualization of Structural Dynamics of Porous Coordination Polymers Induced External Stimuli

• Project Area: Soft Crystals: Science and Photofunctions of Easy-Responsive Systems with Felxibility and Higher-Ordering
• Project/Area Number: 20H04669
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: Nagoya University
• Principal Investigator: 内橋 貴之 名古屋大学, 理学研究科, 教授 (30326300)
• Project Period (FY): 2020-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000); Fiscal Year 2021: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000); Fiscal Year 2020: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: 高速原子間力顕微鏡 / ソフトクリスタル / ピラーアレーン / 低分子ゲル化剤 / 多孔性結晶 / 構造変化 / MOF / MMF / 分子分解能イメージング

Outline of Research at the Start

吸着分離材、不均一系触媒などの多くの応用が期待されている多孔性結晶は、ゲスト分子の吸着や圧力、電場などの外的刺激に応答して結晶構造が柔軟に変化する。本研究では、外的刺激に応答する多孔性結晶表面のナノスケールダイナミクス現象を高速原子間力顕微鏡（AFM）で直接可視化し、I: MMFやMOFなど多孔性結晶へのゲスト分子の吸着と格子歪の結晶表面伝搬の可視化、II: MMF表面での金ナノ粒子の成長過程の追跡、III: 局所力学刺激による格子歪誘起と選択的ゲスト分子の吸着制御の３項目について研究を行い、多孔性結晶の機能設計や性能向上のために基盤的知見を得る。

Outline of Annual Research Achievements

*多孔性結晶の高解像可視化技術の確立.
当初目的としていたMOF結晶はDMF中での観察が結晶の安定化のために必須であるが、DMF中ではMOF結晶表面に数nmスケールの汚染物質が付着していることが判明し、汚染物質を除去できないことからMOF結晶のAFM観察は断念した。そこで、水中でも結晶が安定なピラーアレーン結晶表面での測定を試み、いくつかの結晶で結晶格子像を得ることができ、さらにステップ端面での分子の脱離と再結合などの興味深いダイナミクスを観察できた(A01 生越Gとの共同研究)。
*高速AFMのソフトクリスタルへの応用
領域内外の研究グループとの共同研究により高速AFM技術を様々なソフトクリスタル材料に応用した。当初目的としていたMMF結晶表面での金微粒子の成長過程のリアルタイム観察については成功し、論文としてまとめた。領域内共同研究として、ポルフィリン誘導体による超分子螺旋集合体の形成と融解過程の観察 (A02 杉安Gとの共同研究)や有機分子により触媒される金微粒子の成長過程の観察(A01 楽Gとの共同研究)に成功した。また、低分子ゲル化剤として機能するUrea-C13のゲル化初期過程の高速AFM観察を行ったところ、Urea-C13はグラファイト基板で単分子鎖膜を速やかに形成したあとに、単分子鎖が数本集合した中間ファイバーを経て、さらに太いバンドルファイバーを形成することがわかった。太いバンドルファイバーがゲルの直接的な構成要素であり、平均速度0.05 nm/sで非常に遅い速度で伸長と停止を繰り返しながら成長することがわかった。また、この伸長と停止を伴う成長様式をファイバー端面への分子の結合とバンドルによる安定化によって説明できることが数理モデルにより明らかにした(A03 山中Gとの共同研究)。

Research Progress Status

令和3年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和3年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] Shape-selective one-step synthesis of branched gold nanoparticles on the crystal surface of redox-active Pd^II-macrocycles (2022)
  • Author(s): Yamashita Yutaro、Tashiro Shohei、Ishii Yoshiki、Uchihashi Takayuki、Matsushita Nobuyuki、Kubota Ryou、Shionoya Mitsuhiko
  • Journal Title: Dalton Transactions Volume: 51 Issue: 4 Pages: 1318-1324
  • DOI: 10.1039/d1dt03973c
  • Peer Reviewed
• [Journal Article] Protein Needles Designed to Self‐Assemble through Needle Tip Engineering (2022)
  • Author(s): Kikuchi Kosuke、Fukuyama Tatsuya、Uchihashi Takayuki、Furuta Tadaomi、Maeda Yusuke T.、Ueno Takafumi
  • Journal Title: Small Volume: 18 Issue: 10 Pages: 2106401-2106401
  • DOI: 10.1002/smll.202106401
  • Peer Reviewed
• [Journal Article] Quantitative Visualization of the Interaction between Complement Component C1 and Immunoglobulin G: The Effect of CH1 Domain Deletion (2022)
  • Author(s): Yanaka Saeko、Nishiguchi Shigetaka、Yogo Rina、Watanabe Hiroki、Shen Jiana、Yagi Hirokazu、Uchihashi Takayuki、Kato Koichi
  • Journal Title: International Journal of Molecular Sciences Volume: 23 Issue: 4 Pages: 2090-2090
  • DOI: 10.3390/ijms23042090
  • Peer Reviewed / Open Access
• [Journal Article] JRAB/MICAL-L2 undergoes liquid-liquid phase separation to form tubular recycling endosomes (2021)
  • Author(s): Sakane Ayuko、Yano Taka-aki、Uchihashi Takayuki、Horikawa Kazuki、Hara Yusuke、Imoto Issei、Kurisu Shusaku、Yamada Hiroshi、Takei Kohji、Sasaki Takuya
  • Journal Title: Communications Biology Volume: 4 Issue: 1 Pages: 551-551
  • DOI: 10.1038/s42003-021-02080-7
  • Peer Reviewed / Open Access
• [Journal Article] Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images (2021)
  • Author(s): Bhaskar Dasgupta, Osamu Miyashita, Takayuki Uchihashi and Florence Tama
  • Journal Title: Frontiers in in Molecular Biosciences: Biological Modeling and Simulation Volume: 8 Pages: 704274-704274
  • DOI: 10.3389/fmolb.2021.704274
  • Peer Reviewed / Open Access
• [Journal Article] Tardigrade Secretory-Abundant Heat-Soluble Protein Has a Flexible β-Barrel Structure in Solution and Keeps This Structure in Dehydration (2021)
  • Author(s): Kazuhisa Miyazawa, Satoru G. Itoh, Hiroki Watanabe, Takayuki Uchihashi, Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, Kazuharu Arakawa, and Hisashi Okumura
  • Journal Title: Journal of Physical Chemistry B Volume: 125 Issue: 32 Pages: 9145-9154
  • DOI: 10.1021/acs.jpcb.1c04850
  • Peer Reviewed
• [Journal Article] Deformation of microtubules regulates translocation dynamics of kinesin (2021)
  • Author(s): Syeda Rubaiya Nasrin, Christian Ganser, Seiji Nishikawa, Arif Md Rashedul Kabir, Kazuki Sada, Takefumi Yamashita, Mitsunori Ikeguchi, Takayuki Uchihashi, Henry Hess, Akira Kakugo
  • Journal Title: Sci Adv Volume: 7 Issue: 42 Pages: 1-11
  • DOI: 10.1126/sciadv.abf2211
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Desiccation-induced fibrous condensation of CAHS protein from an anhydrobiotic tardigrade (2021)
  • Author(s): Yagi-Utsumi Maho、Aoki Kazuhiro、Watanabe Hiroki、Song Chihong、Nishimura Seiji、Satoh Tadashi、Yanaka Saeko、Ganser Christian、Tanaka Sae、Schnapka Vincent、Goh Ean Wai、Furutani Yuji、Murata Kazuyoshi、Uchihashi Takayuki、Arakawa Kazuharu、Kato Koichi
  • Journal Title: Scientific Reports Volume: 11 Issue: 1 Pages: 21328-21328
  • DOI: 10.1038/s41598-021-00724-6
  • Peer Reviewed / Open Access
• [Journal Article] Construction of ferritin hydrogels utilizing subunit_subunit interactions (2021)
  • Author(s): Masaru Yamanaka, Tsuyoshi Mashima, Michio Ogihara, Mei Okamoto, Takayuki Uchihashi, and Shun Hirota
  • Journal Title: PLoS ONE Volume: 16 Issue: 11 Pages: e0259052-e0259052
  • DOI: 10.1371/journal.pone.0259052
  • Peer Reviewed / Open Access
• [Journal Article] Molecular Origin of the Anomalous pH Effect in Blue Proteorhodopsin (2021)
  • Author(s): Mizuki Sumikawa, Rei Abe-Yoshizumi, Takayuki Uchihashi, and Hideki Kandori
  • Journal Title: Journal of Physical Chemistry Letters Volume: 12 Issue: 51 Pages: 12225-12229
  • DOI: 10.1021/acs.jpclett.1c03355
  • Peer Reviewed
• [Journal Article] Non-close-packed arrangement of soft elastomer microspheres on solid substrates (2021)
  • Author(s): Yuma Sasaki, Seina Hiroshige, Masaya Takizawa, Yuichiro Nishizawa, Takayuki Uchihashi, Haruka Minato and Daisuke Suzuki
  • Journal Title: RSC Advances Volume: 11 Issue: 24 Pages: 14562-14567
  • DOI: 10.1039/d1ra02688g
  • Peer Reviewed / Open Access
• [Journal Article] Nanostructure and thermoresponsiveness of poly(N-isopropyl methacrylamide)-based hydrogel microspheres prepared via aqueous free radical precipitation polymerization (2021)
  • Author(s): Nishizawa Yuichiro、Minato Haruka、Inui Takumi、Saito Ikuma、Kureha Takuma、Shibayama Mitsuhiro、Uchihashi Takayuki、Suzuki Daisuke
  • Journal Title: RSC Advances Volume: 11 Issue: 22 Pages: 13130-13137
  • DOI: 10.1039/d1ra01650d
  • Peer Reviewed / Open Access
• [Journal Article] Dynamic Assembly/Disassembly of Staphylococcus aureus FtsZ Visualized by High-Speed Atomic Force Microscopy (2021)
  • Author(s): Fujita Junso、Sugiyama Shogo、Terakado Haruna、Miyazaki Maho、Ozawa Mayuki、Ueda Nanami、Kuroda Natsuko、Tanaka Shun-ichi、Yoshizawa Takuya、Uchihashi Takayuki、Matsumura Hiroyoshi
  • Journal Title: International Journal of Molecular Sciences Volume: 22 Issue: 4 Pages: 1697-1697
  • DOI: 10.3390/ijms22041697
  • Peer Reviewed / Open Access
• [Journal Article] Single-molecule level dynamic observation of disassembly of the apo-ferritin cage in solution (2020)
  • Author(s): Maity Basudev、Li Zhipeng、Niwase Kento、Ganser Christian、Furuta Tadaomi、Uchihashi Takayuki、Lu Diannan、Ueno Takafumi
  • Journal Title: Physical Chemistry Chemical Physics Volume: 22 Issue: 33 Pages: 18562-18572
  • DOI: 10.1039/d0cp02069a
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Nanostructures, Thermoresponsiveness, and Assembly Mechanism of Hydrogel Microspheres during Aqueous Free-Radical Precipitation Polymerization (2020)
  • Author(s): Nishizawa Yuichiro、Minato Haruka、Inui Takumi、Uchihashi Takayuki、Suzuki Daisuke
  • Journal Title: Langmuir Volume: 37 Issue: 1 Pages: 151-159
  • DOI: 10.1021/acs.langmuir.0c02654
  • Peer Reviewed
• [Journal Article] Novel Babesia bovis exported proteins that modify properties of infected red blood cells (2020)
  • Author(s): Hakimi H, Templeton TJ, Sakaguchi M, Yamagishi J, Miyazaki S, Yahata K, Uchihashi T, Kawazu SI, Kaneko O, Asada M
  • Journal Title: PLoS Pathogens Volume: 16(10) Issue: 10 Pages: e1008917-e1008917
  • DOI: 10.1371/journal.ppat.1008917
  • NAID: 120006988490
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural insights into the mechanism of rhodopsin phosphodiesterase (2020)
  • Author(s): Ikuta T, Shihoya W, Sugiura M, Yoshida K, Watari M, Tokano T, Yamashita K, Katayama K, Tsunoda SP, Uchihashi T, Kandori H and Nureki O.
  • Journal Title: Nat. Commun. Volume: 11 Issue: 1 Pages: 5605-5605
  • DOI: 10.1038/s41467-020-19376-7
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Convergent evolution of processivity in bacterial and fungal cellulases (2020)
  • Author(s): Uchiyama, T., Uchihashi, T., Nakamura, A., Watanabe, H., Kaneko, S., Samejima, M., and Igarashi K.
  • Journal Title: Proc. Nat. Acad. Sci. U.S.A. Volume: 117 Issue: 33 Pages: 19896-19903
  • DOI: 10.1073/pnas.2011366117
  • Peer Reviewed / Open Access
• [Journal Article] Direct visualization of the conformational change of FUS/TLS upon binding to promoter-associated non-coding RNA (2020)
  • Author(s): Nesreen Hamad, Hiroki Watanabe, Takayuki Uchihashi, Riki Kurokawa, Takashi Nagata, and Masato Katahira
  • Journal Title: Chemical Communications Volume: 56 Issue: 64 Pages: 9134-9137
  • DOI: 10.1039/d0cc03776a
  • Peer Reviewed / Open Access
• [Journal Article] Structural Dynamics of a Protein Domain Relevant to the Water-Oxidizing Complex in Photosystem II as Visualized by High-Speed Atomic Force Microscopy (2020)
  • Author(s): Tokano Takaya、Kato Yuki、Sugiyama Shogo、Uchihashi Takayuki、Noguchi Takumi
  • Journal Title: The Journal of Physical Chemistry B Volume: 124 Issue: 28 Pages: 5847-5857
  • DOI: 10.1021/acs.jpcb.0c03892
  • Peer Reviewed
• [Journal Article] Assembly mechanism of a supramolecular MS-ring complex to initiate bacterial flagellar biogenesis in Vibrio species. (2020)
  • Author(s): Terashima H, Hirano K, Inoue Y, Tokano T, Kawamoto A, Kato T, Yamaguchi E, Namba K, Uchihashi T, Kojima S, Homma M.
  • Journal Title: Journal of Bacteriology Volume: - Issue: 16
  • DOI: 10.1128/jb.00236-20
  • Peer Reviewed
• [Journal Article] Thermoresponsive structural changes of single poly(N-isopropyl acrylamide) hydrogel microspheres under densely packed conditions on a solid substrate (2020)
  • Author(s): Minato Haruka、Nishizawa Yuichiro、Uchihashi Takayuki、Suzuki Daisuke
  • Journal Title: Polymer Journal Volume: 52 Issue: 9 Pages: 1137-1141
  • DOI: 10.1038/s41428-020-0372-3
  • NAID: 40022335719
  • Peer Reviewed
• [Journal Article] Dynamic behavior of an artificial protein needle contacting a membrane observed by high-speed atomic force microscopy (2020)
  • Author(s): Ueno Takafumi、Niwase Kento、Tsubokawa Daisho、Kikuchi Kosuke、Takai Natsumi、Furuta Tadaomi、Kawano Ryuji、Uchihashi Takayuki
  • Journal Title: Nanoscale Volume: in press Issue: 15 Pages: 8166-8173
  • DOI: 10.1039/d0nr01121e
  • Peer Reviewed
• [Presentation] 高速原子間力顕微鏡で可視化する生体/人工分子の一分子ダイナミクス (2022)
  • Author(s): 内橋貴之
  • Organizer: 明治薬科大学大学院フロンティアシンポジウム: 生命への架け橋
  • Invited
• [Presentation] 高速原子間力顕微鏡で撮影するタンパク質の機能動態 (2021)
  • Author(s): 内橋貴之
  • Organizer: 第21回 日本蛋白質科学会年会： WS5. 高速分子動画：タンパク質の構造機能相関研究の最先端
  • Invited
• [Presentation] 高速AFMによる高分子ゲル微粒子の構造物性動態イメージング (2021)
  • Author(s): 内橋貴之
  • Organizer: 第70回高分子討論会: S6. ソフトマテリアルイメージングの最前線
  • Invited
• [Presentation] 高速AFMによる酸素発生光化学系II のドメイン構造揺らぎの可視化 (2020)
  • Author(s): 内橋貴之
  • Organizer: ブルカージャパン オンラインシンポジウム ～単一生体分子の動的プロセス評価に向けた高速AFM技術～
  • Invited
• [Presentation] 高速原子間力顕微鏡でタンパク質の一分子動態を可視化する (2020)
  • Author(s): 内橋貴之
  • Organizer: 新学術領域合同シンポジウム－ソフトロボット学と発動分子科学の境界
  • Invited
• [Presentation] 高速原子間力顕微鏡で可視化する生体・人工分子のダイナミクス (2020)
  • Author(s): 内橋貴之
  • Organizer: 岡山大学大学院医歯薬学総合研究科(薬学系) 先端薬学特論 公開セミナー
  • Invited
• [Presentation] HS-AFM as a versatile tool to study dynamical and mechanical properties of proteins (2020)
  • Author(s): Christian Ganser, Kimitoshi Takeda, Ryota Iino, Koichi Kato and Takayuki Uchihashi
  • Organizer: 第58回日本生物物理学会年会: Symposium "The Multiple Modes of Proteins ? From Molecular Dynamics to Pathogenesis -
  • Int'l Joint Research / Invited
• [Presentation] 高速原子間顕微鏡による膜輸送装置Secの動態観察 (2020)
  • Author(s): 長池航, 板家成良, 春山隆充, 塚崎智也, 内橋貴之
  • Organizer: 日本生体エネルギー研究会第46回討論会
• [Presentation] 高速原子間力顕微鏡を用いた光化学系IIの動態観察 (2020)
  • Author(s): 戸叶貴也, 加藤祐樹, 杉山翔吾, 野口巧, 内橋貴之
  • Organizer: 日本生体エネルギー研究会第46回討論会
• [Presentation] Observation of Substrate Binding Sec Translocon and Structural Change of SecA with HS-AFM (2020)
  • Author(s): Wataru Nagaike, Takamitsu Haruyama, Tomoya Tsukazaki and Takayuki Uchihashi
  • Organizer: 第58回日本生物物理学会年会
  • Int'l Joint Research
• [Presentation] 溶液中HS-AFM observation of Amyloid β elongation and inhibition by antibodies (2020)
  • Author(s): Shogo Miyajima, Maho Yagi-Utsumi, Takayuki Uchihashi and Koichi Kato
  • Organizer: 第58回日本生物物理学会年会
  • Int'l Joint Research
• [Presentation] Chasing the transformation between monomer and dimer structure of cadherin anchored to supported lipid bilayer by high-speed AFM (2020)
  • Author(s): Shigetaka Nishiguchi, Hiroki Oda and Takayuki Uchihashi
  • Organizer: 第58回日本生物物理学会年会
  • Int'l Joint Research
• [Book] 図説 表面分析ハンドブック (2021)
  • Author(s): 日本表面真空学会
  • Total Pages: 576
  • Publisher: 朝倉書店
  • ISBN: 9784254201703
• [Remarks] 名古屋大学D研ホームページ
  • URL: http://d.phys.nagoya-u.ac.jp/